Non-invasive fluorescence imaging is an important technique in biology. However, detection of traditional biomarker emissions is accompanied by a high background signal. In this study we examined whether upconversion sodium yttrium fluoride (NaYF4) nanocrystals were suitable for autofluorescence-free multicolor fluorescence imaging in a living animal. Tissue autofluorescence was induced with a 405 nm light source, then rats were subjected to injection of fluorescein isothiocyanate (FITC), cadmium selenide/zinc sulfide (CdSe/ZnS) quantum dots (QDs), or NaYF4:ytterbium/thulium (Yb3+/Tm3+), NaYF4:Yb3+/holmium (Ho3+), and NaYF4:Yb3+/Ho3+/cerium (Ce3+) nanocrystals. Imaging with NaYF4 nanocrystals (974 nm laser) completely removed the high tissue autofluorescence, in marked contrast to imaging with FITC and QDs (405 nm light). Optical imaging experiments demonstrated that multiple biological targets and organs could be imaged at the same time using multicolor NaYF4 upconversion nanocrystals under a single excitation wavelength (974 nm). These data demonstrated the proof-of-principle that autofluorescence-free multicolor imaging using near-infrared to visible upconversion of NaYF4 nanocrystals excited by laser can be performed in a living animal.